Semi-volatile pollutants can undergo long-range atmospheric transport from low-altitude source regions to high-altitude regions and then accumulate in surface matrices (soil and plants). The Himalayas is the highest mountain range worldwide, but there have been limited studies on the source, transport, and deposition of polycyclic aromatic hydrocarbons (PAHs) and mercury (Hg) in the region. In this study, atmospheric PAHs, and the PAHs and Hg in soil and foliage were determined along a transect on a southern slope of the Himalayas, Nepal. The study showed anthropogenic emissions of PAHs and Hg occurred in the lowland areas of Nepal, and upslope transport to the high-altitude regions happened for both pollutants. During the upslope transport, forest filter effect and snow scavenging may be the important factors that enhance the deposition of PAHs, contributing to the negative pattern between concentrations of PAHs and altitudes. On the contrary, more Hg accumulated in the high Himalayas, relating to the enhanced deposition in the high altitude caused by the higher input from upper atmosphere.